(2li) Utilizing Microbial Communities for Valorization of Waste Carbon

An underpinning of sustainable chemistry is the minimization or (re)utilization of waste streams, moving towards closed cycles. In the context of complex and heterogeneous waste streams, biological systems have been proposed as a solution for upgrading waste materials to value-added products, owing to the ability of microbial metabolism to "funnel" heterogenous carbon sources to tractable starting points for biochemical synthesis. This approach has relevance in multiple contexts including biomass processing (e.g. lignin), food and agricultural waste (e.g. volatile fatty acids), and municipal waste (mixed organic-plastic streams), among others. For these applications, an emerging solution is the use of synthetically designed microbial communities (SynComs) that leverage the traits and interactions of multiple microbial species to accomplish complex tasks, inspired by natural systems. While exploration of SynComs for this application, and more broadly Metabolic Engineering as a whole, has begun, these initial experiments: 1) are highly reliant on model microbes like Escherichia coli and Saccharomyces cerevisiae and thus miss out on a vast array of genetic function and 2) fail to incorporate ecological principles to SynCom construction and thus produce SynCom with tenuous stability. The planned initial work of my laboratory will address these shortcomings. Expressly, my lab's initial aims are:

• To apply ecological principles to construct stable synthetic communities of genetically and functionally diverse microbial species for metabolic engineering applications
• To develop genetic tools for engineering these genetically diverse microbial species
• To apply these novel synthetic communities in waste valorization processes
• Lastly, to leverage existing chemical species within the waste streams for (bio)chemically advantaged synthesis processes in the context of waste valorization

Research Experience

My research trajectory began in earnest after the completion of my Masters in Biotechnology, during my time in industry at the Metabolic Engineering firm Manus Bio. At Manus, I gained critical exposure to the upgrading of waste materials (glycerol), utilization of key biochemical steps (P450 oxygenation chemistry), and what it looks like to conduct research that requires scaling. Following, I returned to Northwestern University to pursue a doctorate in Chemical Engineering. During my time in Keith Tyo's lab, I gained experience developing genetic tools for non-model organisms (Acinetobacter baylyi ADP1) and with valorization of additional waste streams (lignin), along with significant experience in protein engineering and biochemical pathway design. After my doctorate, I began a postdoc in Adam Arkin's lab at Lawrence Berkeley National Lab/University of California Berkeley. In the Arkin lab, my research has focused on the study of synthetic microbial communities to understand a contaminated field site and the application of high-throughput genetics for identification of gene function. For both projects, I have gained significant experience in systems biology and ecology.

Teaching Interests

While I am able to teach all fundamental Chemical Engineering courses, I have particular experience and research overlap in Energy and Mass Balances, Kinetics, Mass transfer, and Reactor Design. In addition, I could readily instruct the latter three courses at the graduate level. During my doctorate, I was a teaching assistant for a graduate level Kinetics and Reactor Design course. In addition, during my doctorate I completed a teaching apprentice, teaching multiple lectures and designing homework and test questions for Mass and Energy Balances (Introduction to Chemical Engineering). Beyond core Chemical Engineering courses, I hope to develop special topics courses relevant to my research interests in metabolic engineering, synthetic biology, protein engineering, and sustainability.

Selected publications: (Total 13, 7 first-author, 4 second-author, H-index 10)

• Bradley W. Biggs, Hal S. Alper, Brian F. Pfleger, Keith E.J. Tyo, Christine N.S. Santos, Parayil Kumaran Ajikumar, Gregory Stephanopoulos. Enabling commercial success of industrial biotechnology. Science. 2022.
• Bradley W. Biggs, Chin Giaw Lim, Kristen Sagliani, Smriti Shankar, Gregory Stephanopoulos, Marjan De Mey, Parayil Kumaran Ajikumar. Overcoming Heterologous Protein Interdependency to Optimize P450-Mediated Taxol Precursor Synthesis in Escherichia coli. Proceedings of the National Academy of Sciences (USA). 2016.
• Bradley W. Biggs, Stacy Bedore, Erika Arvay, Shu Huang, Harshith Subramanian, Emily A. McIntyre, Chantel V. Duscent-Maitland, Ellen L. Neidle, and Keith E.J. Tyo. Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1. Nucleic Acids Research. 2020.
• Bradley Walters Biggs, Brecht De Paepe, Christine Nicole S. Santos, Marjan De Mey, and Parayil Kumaran Ajikumar. Multivariate modular metabolic engineering for pathway and strain optimization. Current Opinion in Biotechnology. 2014.